core::chemical::Metapatch Class Reference

A class patching basic ResidueType to create variant types, containing multiple PatchCase. More...

#include <Metapatch.hh>

Inheritance diagram for core::chemical::Metapatch:

Public Member Functions
virtual	~Metapatch ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...
void	read_file (std::string const &filename)
	constructor from file More...
virtual bool	applies_to (ResidueType const &rsd) const
	can I operate on this residue type? More...
utility::vector1< PatchOP >	generate_patches (ResidueType const &rsd_type) const
	returns patched residue, 0 if patch failed More...
PatchOP	get_one_patch (ResidueType const &rsd_type, std::string const &atom_name) const
bool	meets_requirements (ResidueType const &r, Size i) const
virtual std::string const &	name () const
	unique name of this patch, eg Nter-simple, Cter-full, Phospho, ... ? More...
virtual utility::vector1 < std::string > const &	types () const
	the variant types created by applying this patch More...
utility::vector1< std::string >	atoms (ResidueType const &rsd_type) const

Private Attributes
std::string	name_
	private data More...
utility::vector1< std::string >	types_
	variant types created by the created patches More...
utility::vector1< PatchCaseOP >	cases_
	different cases to which the derived patches patch will be applied slightly differently, e.g., N-terminus patch to PRO and GLY More...
chemical::AtomProperty	pertinent_property_
utility::vector1< std::string >	case_lines_
ResidueTypeSelector	selector_
	criteria to select ResidueTypes to which the patches are applied More...

Detailed Description

A class patching basic ResidueType to create variant types, containing multiple PatchCase.

Definition at line 33 of file Metapatch.hh.

Constructor & Destructor Documentation

core::chemical::Metapatch::~Metapatch ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 40 of file Metapatch.cc.

Member Function Documentation

virtual bool core::chemical::Metapatch::applies_to ( ResidueType const &  rsd ) const

inlinevirtual

can I operate on this residue type?

Definition at line 44 of file Metapatch.hh.

References selector_.

Referenced by generate_patches().

utility::vector1< std::string > core::chemical::Metapatch::atoms

(

ResidueType const &

rsd_type

)

const

Definition at line 170 of file Metapatch.cc.

References core::chemical::ResidueType::atom_name(), core::chemical::get_patch_names(), meets_requirements(), core::chemical::ResidueType::name3(), and core::chemical::ResidueType::natoms().

utility::vector1< PatchOP > core::chemical::Metapatch::generate_patches

(

ResidueType const &

rsd_type

)

const

returns patched residue, 0 if patch failed

Definition at line 197 of file Metapatch.cc.

References applies_to(), core::chemical::ResidueType::atom_name(), core::chemical::case_from_lines(), case_lines_, core::chemical::get_patch_names(), meets_requirements(), core::chemical::ResidueType::name3(), name_, core::chemical::ResidueType::natoms(), and selector_.

PatchOP core::chemical::Metapatch::get_one_patch	(	ResidueType const &	rsd_type,
		std::string const &	atom_name
	)		const

Definition at line 136 of file Metapatch.cc.

References core::chemical::case_from_lines(), case_lines_, core::chemical::ResidueType::name3(), name_, and selector_.

bool core::chemical::Metapatch::meets_requirements ( ResidueType const &  r, Size  i  ) const

inline

Definition at line 58 of file Metapatch.hh.

References core::chemical::ResidueType::atom(), core::chemical::Atom::has_property(), and pertinent_property_.

Referenced by atoms(), and generate_patches().

virtual std::string const& core::chemical::Metapatch::name ( ) const

inlinevirtual

unique name of this patch, eg Nter-simple, Cter-full, Phospho, ... ?

Definition at line 67 of file Metapatch.hh.

References name_.

void core::chemical::Metapatch::read_file

(

std::string const &

filename

)

constructor from file

• first read in all lines from the file, discarding # comment lines
• parse input lines for Metapatch name and variant types (NAME, TYPES)
• parse input lines for general ResidueTypeSelector defined for this Patch (BEGIN_SELECTOR, END_SELECTOR)
• parse input lines to create each case accordingly (BEGIN_CASE, END_CASE)

  Note

  keep the order to avoid triggering parsing errors

Definition at line 50 of file Metapatch.cc.

References core::chemical::ResidueTypeSelector::add_line(), core::chemical::case_from_lines(), case_lines_, cases_, core::chemical::ResidueTypeSelector::clear(), name_, pertinent_property_, core::chemical::AtomPropertiesManager::property_from_string(), selector_, core::scoring::hbonds::t(), core::chemical::tag_from_line(), core::chemical::tr(), and types_.

virtual utility::vector1< std::string > const& core::chemical::Metapatch::types ( ) const

inlinevirtual

the variant types created by applying this patch

Definition at line 75 of file Metapatch.hh.

References types_.

Member Data Documentation

utility::vector1< std::string > core::chemical::Metapatch::case_lines_

private

Definition at line 96 of file Metapatch.hh.

Referenced by generate_patches(), get_one_patch(), and read_file().

utility::vector1< PatchCaseOP > core::chemical::Metapatch::cases_

private

different cases to which the derived patches patch will be applied slightly differently, e.g., N-terminus patch to PRO and GLY

Definition at line 92 of file Metapatch.hh.

Referenced by read_file().

std::string core::chemical::Metapatch::name_

private

private data

name of the patch

Definition at line 86 of file Metapatch.hh.

Referenced by generate_patches(), get_one_patch(), name(), and read_file().

chemical::AtomProperty core::chemical::Metapatch::pertinent_property_

private

Definition at line 94 of file Metapatch.hh.

Referenced by meets_requirements(), and read_file().

ResidueTypeSelector core::chemical::Metapatch::selector_

private

criteria to select ResidueTypes to which the patches are applied

Definition at line 99 of file Metapatch.hh.

Referenced by applies_to(), generate_patches(), get_one_patch(), and read_file().

utility::vector1< std::string > core::chemical::Metapatch::types_

private

variant types created by the created patches

Definition at line 89 of file Metapatch.hh.

Referenced by read_file(), and types().

---

The documentation for this class was generated from the following files:

• src/core/chemical/Metapatch.hh
• src/core/chemical/Metapatch.cc